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- PDB-8cd3: Crystal structure of human Scribble PDZ1 domain in complex with h... -

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Basic information

Entry
Database: PDB / ID: 8cd3
TitleCrystal structure of human Scribble PDZ1 domain in complex with human TMIGD1
Components
  • Protein scribble homolog
  • Transmembrane and immunoglobulin domain-containing protein 1
KeywordsPROTEIN BINDING / PDZ domain / cell polarity / Scribble / transmembrane protein
Function / homology
Function and homology information


neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / extrinsic component of postsynaptic density membrane / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / Scrib-APC-beta-catenin complex / astrocyte cell migration / synaptic vesicle targeting / polarized epithelial cell differentiation ...neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / extrinsic component of postsynaptic density membrane / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / Scrib-APC-beta-catenin complex / astrocyte cell migration / synaptic vesicle targeting / polarized epithelial cell differentiation / epithelial structure maintenance / myelin sheath abaxonal region / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to adherens junction / cell-cell contact zone / mammary gland duct morphogenesis / post-anal tail morphogenesis / establishment or maintenance of epithelial cell apical/basal polarity / activation of GTPase activity / auditory receptor cell stereocilium organization / regulation of postsynaptic neurotransmitter receptor internalization / RND2 GTPase cycle / RND3 GTPase cycle / positive chemotaxis / positive regulation of receptor recycling / receptor clustering / RHOJ GTPase cycle / negative regulation of activated T cell proliferation / RHOQ GTPase cycle / CDC42 GTPase cycle / negative regulation of mitotic cell cycle / immunological synapse / synaptic vesicle endocytosis / signaling adaptor activity / neural tube closure / Asymmetric localization of PCP proteins / adherens junction / wound healing / cell-cell adhesion / positive regulation of type II interferon production / cell-cell junction / cell migration / cell junction / lamellipodium / presynapse / basolateral plasma membrane / cell population proliferation / postsynaptic density / cadherin binding / positive regulation of apoptotic process / glutamatergic synapse / protein kinase binding / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
: / Leucine-rich repeats, bacterial type / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / Leucine-rich repeat / PDZ domain profile. ...: / Leucine-rich repeats, bacterial type / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / Leucine-rich repeat / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Protein scribble homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMaddumage, J.C. / Kvansakul, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1103871 Australia
CitationJournal: Commun Biol / Year: 2023
Title: Membrane recruitment of the polarity protein Scribble by the cell adhesion receptor TMIGD1.
Authors: Thuring, E.M. / Hartmann, C. / Maddumage, J.C. / Javorsky, A. / Michels, B.E. / Gerke, V. / Banks, L. / Humbert, P.O. / Kvansakul, M. / Ebnet, K.
History
DepositionJan 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Protein scribble homolog
A: Transmembrane and immunoglobulin domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)11,7472
Polymers11,7472
Non-polymers00
Water1,11762
1
B: Protein scribble homolog
A: Transmembrane and immunoglobulin domain-containing protein 1

B: Protein scribble homolog
A: Transmembrane and immunoglobulin domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)23,4944
Polymers23,4944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554-x+1/2,y,-z-1/41
Buried area3500 Å2
ΔGint-11 kcal/mol
Surface area11840 Å2
Unit cell
Length a, b, c (Å)53.664, 53.664, 215.703
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-949-

HOH

21A-103-

HOH

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Components

#1: Protein Protein scribble homolog / Scribble / hScrib / Protein LAP4


Mass: 10877.308 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCRIB, CRIB1, KIAA0147, LAP4, SCRB1, VARTUL / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q14160
#2: Protein/peptide Transmembrane and immunoglobulin domain-containing protein 1


Mass: 869.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.88 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 24% w/v PEG 1500, 20% Ethylene Glycol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.9→43.01 Å / Num. obs: 13031 / % possible obs: 100 % / Redundancy: 26.1 % / Biso Wilson estimate: 30.37 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.078 / Net I/σ(I): 21.7
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 809 / CC1/2: 0.921

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→43.01 Å / SU ML: 0.2124 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.8127
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2225 659 5.07 %
Rwork0.1962 12344 -
obs0.1975 13003 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.22 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms809 0 0 62 871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011818
X-RAY DIFFRACTIONf_angle_d1.28381104
X-RAY DIFFRACTIONf_chiral_restr0.0793127
X-RAY DIFFRACTIONf_plane_restr0.0109147
X-RAY DIFFRACTIONf_dihedral_angle_d6.4011119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.050.24031350.19632389X-RAY DIFFRACTION99.8
2.05-2.250.19031100.16412433X-RAY DIFFRACTION100
2.25-2.580.23191220.17992445X-RAY DIFFRACTION100
2.58-3.250.20771380.20922464X-RAY DIFFRACTION100
3.25-43.010.22921540.2012613X-RAY DIFFRACTION99.96
Refinement TLS params.Method: refined / Origin x: 11.9646087635 Å / Origin y: -0.23275637232 Å / Origin z: -12.5611567071 Å
111213212223313233
T0.212287145933 Å2-0.0411703448049 Å20.00649696945074 Å2-0.272864976467 Å2-0.0206117855479 Å2--0.249265906448 Å2
L0.317988412529 °2-0.168183436364 °2-0.390769756866 °2-0.721289025899 °2-0.134731367841 °2--0.664043772467 °2
S0.0501548581327 Å °0.0859594845887 Å °0.0164795344445 Å °0.0185924838553 Å °-0.0669212354309 Å °0.16926651931 Å °0.0438629954547 Å °-0.089547761913 Å °-0.000598843734905 Å °
Refinement TLS groupSelection details: all

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